Liliana M. Dávalos

The nature and dynamics of bacterial genomes.

Though generally small and gene rich, bacterial genomes are constantly subjected to both mutational and population-level processes that operate to increase amounts of functionless DNA. As a result, the coding potential of bacterial genomes can be substantially lower than originally predicted. Whereas only a single pseudogene was included in the original annotation of the bacterium Escherichia coli, we estimate that this genome harbors hundreds of inactivated and otherwise functionless genes. Such regions will never yield a detectable phenotype, but their identification is vital to efforts to elucidate the biological role of all the proteins within the cell.

Forests and drugs: coca-driven deforestation in tropical biodiversity hotspots.

Identifying drivers of deforestation in tropical biodiversity hotspots is critical to assess threats to particular ecosystems and species and proactively plan for conservation. We analyzed land cover change between 2002 and 2007 in the northern Andes, Chocó, and Amazon forests of Colombia, the largest producer of coca leaf for the global cocaine market, to quantify the impact of this illicit crop on forest dynamics, evaluate the effectiveness of protected areas in this context, and determine the effects of eradication on deforestation. Landscape-level analyses of forest conversion revealed that proximity to new coca plots and a greater proportion of an area planted with coca increased the probability of forest loss in southern Colombia, even after accounting for other covariates and spatial autocorrelation. We also showed that protected areas successfully reduced forest conversion in coca-growing regions. Neither eradication nor coca cultivation predicted deforestation rates across municipalities. Instead, the presence of new coca cultivation was an indicator of municipalities, where increasing population led to higher deforestation rates. We hypothesize that poor rural development underlies the relationship between population density and deforestation in coca-growing areas. Conservation in Colombias vast forest frontier, which overlaps with its coca frontier, requires a mix of protected areas and strategic rural development to succeed.

Saturation and base composition bias explain phylogenomic conflict in Plasmodium

Despite recent genome-based advances in understanding Plasmodium molecular evolution and its relationship to disease mechanisms and potential drug development, the phylogenetics of the group is currently limited to single-gene analyses. Here we develop and analyze a set of N100 putative orthologous genes derived from genome comparisons. We aimed to minimize systematic errors that arise when reconstructing the Plasmodium phylogeny with a genome-scale data set by evaluating the congruence of different genes, optimality criteria, and models of sequence evolution with previous studies encompassing fewer characters and more species. Saturation in substitutions and bias in base frequencies at third-codon positions characterized most Plasmodium genes. Molecular evolution models that partitioned rates of change by codon position were best at accounting for these sequence characteristics, as were analyses of amino acid alignments. These methods also ameliorated, but did not entirely avoid, the impact of reduced taxon sampling on phylogeny. The use of these models and expanded taxon sampling are necessary to maximize detection of multiple substitutions, overcome compositional biases, and, ultimately, resolve with confidence the phylogeny of Plasmodium.

The San Lucas mountain range in Colombia: how much conservation is owed to the violence?

The imminence of forest conversion in the northern Andean region requires a careful evaluation of the social, political and economic context in which environmental efforts take place in order to achieve conservation. Through its socioeconomic effects violent conflict can result in threats pertinent to both conservation and resource management schemes. A survey of the San Lucas mountain range, at the northern tip of the Colombian Central Andes, is presented as a case study of factors associated with violent conflict that may hinder or enhance conservation in this complex social and political setting. Instability in land use and tenure associated with armed conflict were identified as major pressures associated with further conversion of tropical forest habitats; while low rates of settlement and measures enforced by armed rule were very effective in preserving certain tracts of forest. War certainly alleviates demographic pressure from settlers, but contemporary patterns of colonization in San Lucas suggest that armed conflict is detrimental to conservation purposes and to key members of the biological community.

PHYLOGENY OF THE LONCHOPHYLLINI (CHIROPTERA: PHYLLOSTOMIDAE)

Abstract A combination of 1,140 base pairs of the mitochondrial cytochrome b gene of Platalina, Lionycteris, and several species of Lonchophylla (Chiroptera: Phyllostomidae) with 150 morphological, sex chromosome, and restriction site characters were used in an attempt to resolve relationships among the lonchophylline taxa. In addition, the monophyly of Lonchophylla was tested, particularly with respect to Platalina. The most parsimonious hypothesis of relationships using all available characters was (L. mordax ((L. chocoana (L. robusta, L. handleyi))(L. thomasi (Lionycteris, Platalina)))). Lonchophylla appears to be paraphyletic, but this arrangement is not well supported. Our analyses suggest that Platalina is not simply a large Lonchophylla, as had been suggested by previous morphological analyses. The low support values for basal relationships found in this study are probably caused by saturation in cytochrome b 3rd positions. Additionally, 2 alternative explanations are viable (if improbable): unsampled lonchophyllines are necessary to confidently resolve relationships at the base of the group, or the lack of resolution at the base of the lonchophylline phylogeny might be explained by rapid speciation following the separation from other glossophagines. Future work examining the phylogenetic relationships of lonchophylline bats should focus on describing new taxa, obtaining tissue samples from unsequenced representatives, and adding nuclear loci to this mitochondrial DNA data set.

A New Chocoan Species of Lonchophylla (Chiroptera: Phyllostomidae)

Abstract Lonchophylla is a diverse genus of glossophagines characterized by large, forwardly projecting inner upper incisors and the absence of zygomatic arches. Seven species are currently recognized, including the large-bodied (greatest length of skull >24.5 mm) robusta, handleyi, hesperia, and bokermanni and the small-bodied (greatest length of skull <24.5 mm) thomasi, dekeyseri, and mordax. Lonchophylla species range throughout the Neotropics and include endemics in Amazonia, the Cerrado, and the arid regions of coastal Peru and Ecuador. In this paper I describe a new large-bodied species, Lonchophylla chocoana, from the subtropical rainforests of the Chocó in southwestern Colombia and northwestern Ecuador. I also document the diagnostic external, craniodental, and mitochondrial characters of the new species and summarize morphological characteristics for the new species and its sympatric congeners.

Regulating access to genetic resources under the Convention on Biological Diversity: an analysis of selected case studies

In 1992 parties to the Convention on Biological Diversity (CBD) agreed to develop and implement policies to regulate and facilitate access to genetic resources (AGR). We examine regulations and agreements in Brazil, Colombia, and the Philippines in detail and discuss how these countries are implementing the AGR mandate. In particular, we evaluate progress toward achieving the CBD objectives of conserving biological diversity, using its components in a sustainable manner, and equitably sharing the benefits arising from the use of genetic resources. We highlight the difficulties in developing and implementing these policies, arising from the conflicting goals of regulating and facilitating AGR, as well as the special character of genetic resources, existing ex situ collections, issues of ownership and tenure, and the dearth of legal, institutional, and scientific capacity in many countries. We recommend (1) independent, multidisciplinary evaluation of the success of the access policy in achieving CBD objectives, (2) resolution of the conflict between traditional land tenure and legal property rights of genetic resources so as to match conservation obligations with benefit-sharing rights, (3) recognition that benefits obtained from AGR may be entirely non-monetary, and (4) that countries provide a two-track’ AGR application process separately for commercial and non-commercial users.

Missing the Forest for the Profits: The Role of Multinational Corporations in the International Forest Regime

The international community has placed great hope and invested considerable time in exploring a global forest convention through the United Nations Conference on Environment and Developments Intergovernmental Forum on Forests and the Intergovernmental Panel on Forests process under the Commission on Sustainable Development. Multinational corporations control almost 40% of the world market in forest products, constituting a major stakeholder in global forest policy. The few cases of direct intervention by multinational corporations at international fora suggest their interests are expressed elsewhere. The authors identify and discuss three types of intervention in the existing forest regime: avoidance, enforcement-driven compliance, and performance-driven compliance. The regime has not achieved performance-driven compliance from multinational corporations because the regime itself is weak and has little support from states internationally and domestically. The authors suggest that multinational corporations have been so effective at avoiding or conditioning compliance that incentives for complying fully with the regime are nil.